How to make an object transparent to the freestyle pass?
The source of the problem is that Freestyle view map has (can see) the smoke domain geometry. This is a typical problem. Transparent mesh like glasses can be solved with the same method.


Put torus, cone and sphere on a new render layer (mesh on layer 1). This render layer will be rendered with freestyle.
Isolate the smoke domain cube to another render layer (ie: mesh on layer 2). Turn off freestyle on this render layer or don't render this layer at all.


That should solve the smoke domain cube from being rendered.